[Bioperl-l] filter_by_location in Bio::DB::SeqFeature::Store::memory
Mitch Skinner
mitch_skinner at berkeley.edu
Thu Jan 14 22:10:53 UTC 2010
Hi,
Some people haven't been getting all of the features in their GFF3 into
JBrowse, and a nice test case that James Casbon posted to the list
helped me track it down.
Here's an example of the behavior I was seeing with BioPerl 1.6.1 (using
Devel::REPL):
==============
$ use Bio::DB::SeqFeature::Store
$ my $db = Bio::DB::SeqFeature::Store->new(-adaptor=>"memory",
-dsn=>"casbon.gff3")
$Bio_DB_SeqFeature_Store_memory1 =
Bio::DB::SeqFeature::Store::memory=HASH(0xa27ceec);
$ $db->features(-seq_id=>"CYP2C8")
$ARRAY1 = [
Feature:src(41),
region(CYP2C8),
Feature:src(37),
Feature:src(39),
Feature:src(42),
Feature:src(40),
Feature:src(38)
];
==============
I expected to also see the features with IDs 43 and 44 (the gff3 file is
attached).
I think there's a problem in the filter_by_location method. If start
and end parameters aren't passed to the method, it sets default start
and end values that lead it to examine all of the bins in its index.
But the end value that it creates is at the beginning of the last bin,
and I think it should be at the end of the last bin instead. The
attached patch changes it to be at the end of the last bin.
Regards,
Mitch
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